Multiple sequence alignment - TraesCS3B01G530400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G530400 chr3B 100.000 2288 0 0 1 2288 771413952 771411665 0 4226
1 TraesCS3B01G530400 chr3B 92.848 1538 88 13 1 1520 745588825 745590358 0 2211
2 TraesCS3B01G530400 chr1D 94.473 1538 66 3 1 1520 209755853 209757389 0 2351
3 TraesCS3B01G530400 chr1D 92.263 1551 87 10 1 1520 423893324 423894872 0 2169
4 TraesCS3B01G530400 chr1D 91.528 1558 77 13 1 1520 369900543 369902083 0 2095
5 TraesCS3B01G530400 chr1B 93.762 1539 76 11 1 1520 566609747 566611284 0 2292
6 TraesCS3B01G530400 chr1B 93.303 1538 83 11 1 1520 311135960 311134425 0 2252
7 TraesCS3B01G530400 chr1B 92.541 791 38 10 1515 2288 640421334 640422120 0 1114
8 TraesCS3B01G530400 chr6B 93.502 1539 80 11 1 1520 643872270 643870733 0 2270
9 TraesCS3B01G530400 chr6B 92.691 1546 86 7 1 1520 643648493 643650037 0 2204
10 TraesCS3B01G530400 chr6B 92.746 1544 80 12 1 1520 711404576 711406111 0 2202
11 TraesCS3B01G530400 chr6B 94.057 774 37 7 1520 2288 642989365 642988596 0 1166
12 TraesCS3B01G530400 chr2B 92.788 1539 92 11 1 1520 412262329 412263867 0 2209
13 TraesCS3B01G530400 chr2B 93.086 781 42 8 1517 2288 733993950 733994727 0 1133
14 TraesCS3B01G530400 chr5B 92.073 1539 86 10 1 1520 202892496 202890975 0 2134
15 TraesCS3B01G530400 chr5B 95.472 773 30 4 1520 2288 711263013 711262242 0 1229
16 TraesCS3B01G530400 chr6D 91.212 1559 84 20 1 1520 446604645 446603101 0 2071
17 TraesCS3B01G530400 chr7B 93.357 1400 73 11 140 1520 483869468 483868070 0 2052
18 TraesCS3B01G530400 chr7B 92.874 1277 73 2 1 1259 625709241 625710517 0 1838
19 TraesCS3B01G530400 chr7B 94.723 777 36 3 1517 2288 699819429 699820205 0 1203
20 TraesCS3B01G530400 chr4D 92.851 1077 59 2 1 1059 398284705 398285781 0 1546
21 TraesCS3B01G530400 chr4A 93.830 778 35 6 1517 2288 643570141 643570911 0 1158
22 TraesCS3B01G530400 chr1A 93.888 769 35 9 1520 2288 451855253 451856009 0 1149
23 TraesCS3B01G530400 chr3A 93.238 769 43 6 1520 2288 729744561 729745320 0 1123
24 TraesCS3B01G530400 chr7A 92.506 774 44 10 1516 2288 198228667 198229427 0 1096


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G530400 chr3B 771411665 771413952 2287 True 4226 4226 100.000 1 2288 1 chr3B.!!$R1 2287
1 TraesCS3B01G530400 chr3B 745588825 745590358 1533 False 2211 2211 92.848 1 1520 1 chr3B.!!$F1 1519
2 TraesCS3B01G530400 chr1D 209755853 209757389 1536 False 2351 2351 94.473 1 1520 1 chr1D.!!$F1 1519
3 TraesCS3B01G530400 chr1D 423893324 423894872 1548 False 2169 2169 92.263 1 1520 1 chr1D.!!$F3 1519
4 TraesCS3B01G530400 chr1D 369900543 369902083 1540 False 2095 2095 91.528 1 1520 1 chr1D.!!$F2 1519
5 TraesCS3B01G530400 chr1B 566609747 566611284 1537 False 2292 2292 93.762 1 1520 1 chr1B.!!$F1 1519
6 TraesCS3B01G530400 chr1B 311134425 311135960 1535 True 2252 2252 93.303 1 1520 1 chr1B.!!$R1 1519
7 TraesCS3B01G530400 chr1B 640421334 640422120 786 False 1114 1114 92.541 1515 2288 1 chr1B.!!$F2 773
8 TraesCS3B01G530400 chr6B 643870733 643872270 1537 True 2270 2270 93.502 1 1520 1 chr6B.!!$R2 1519
9 TraesCS3B01G530400 chr6B 643648493 643650037 1544 False 2204 2204 92.691 1 1520 1 chr6B.!!$F1 1519
10 TraesCS3B01G530400 chr6B 711404576 711406111 1535 False 2202 2202 92.746 1 1520 1 chr6B.!!$F2 1519
11 TraesCS3B01G530400 chr6B 642988596 642989365 769 True 1166 1166 94.057 1520 2288 1 chr6B.!!$R1 768
12 TraesCS3B01G530400 chr2B 412262329 412263867 1538 False 2209 2209 92.788 1 1520 1 chr2B.!!$F1 1519
13 TraesCS3B01G530400 chr2B 733993950 733994727 777 False 1133 1133 93.086 1517 2288 1 chr2B.!!$F2 771
14 TraesCS3B01G530400 chr5B 202890975 202892496 1521 True 2134 2134 92.073 1 1520 1 chr5B.!!$R1 1519
15 TraesCS3B01G530400 chr5B 711262242 711263013 771 True 1229 1229 95.472 1520 2288 1 chr5B.!!$R2 768
16 TraesCS3B01G530400 chr6D 446603101 446604645 1544 True 2071 2071 91.212 1 1520 1 chr6D.!!$R1 1519
17 TraesCS3B01G530400 chr7B 483868070 483869468 1398 True 2052 2052 93.357 140 1520 1 chr7B.!!$R1 1380
18 TraesCS3B01G530400 chr7B 625709241 625710517 1276 False 1838 1838 92.874 1 1259 1 chr7B.!!$F1 1258
19 TraesCS3B01G530400 chr7B 699819429 699820205 776 False 1203 1203 94.723 1517 2288 1 chr7B.!!$F2 771
20 TraesCS3B01G530400 chr4D 398284705 398285781 1076 False 1546 1546 92.851 1 1059 1 chr4D.!!$F1 1058
21 TraesCS3B01G530400 chr4A 643570141 643570911 770 False 1158 1158 93.830 1517 2288 1 chr4A.!!$F1 771
22 TraesCS3B01G530400 chr1A 451855253 451856009 756 False 1149 1149 93.888 1520 2288 1 chr1A.!!$F1 768
23 TraesCS3B01G530400 chr3A 729744561 729745320 759 False 1123 1123 93.238 1520 2288 1 chr3A.!!$F1 768
24 TraesCS3B01G530400 chr7A 198228667 198229427 760 False 1096 1096 92.506 1516 2288 1 chr7A.!!$F1 772

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
583 605 0.773644 AGGAGGAACATTGGCAGTGT 59.226 50.0 10.11 10.11 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1893 1.012562 CGACGACGACGATGACGAT 60.013 57.895 15.32 0.0 41.06 3.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 154 2.514592 CCCTACCTGGCATGTGCG 60.515 66.667 5.62 0.00 43.26 5.34
167 169 4.116328 GCGCCGCCTTTTCTTCCC 62.116 66.667 0.00 0.00 0.00 3.97
303 306 1.749634 CTGTTTAGGGTCGTCGGAGAT 59.250 52.381 0.00 0.00 40.67 2.75
387 390 2.755103 TCAGCGTCTTCAGCTCATCTTA 59.245 45.455 0.00 0.00 44.06 2.10
416 419 2.554142 TCATGAGCACGACATTGGATC 58.446 47.619 0.00 0.00 0.00 3.36
491 511 3.782443 GCCGTCCACCCGAGGAAT 61.782 66.667 0.00 0.00 39.92 3.01
572 594 2.068834 TGACGATAGGGAGGAGGAAC 57.931 55.000 0.00 0.00 43.77 3.62
573 595 1.286849 TGACGATAGGGAGGAGGAACA 59.713 52.381 0.00 0.00 43.77 3.18
577 599 2.037772 CGATAGGGAGGAGGAACATTGG 59.962 54.545 0.00 0.00 0.00 3.16
583 605 0.773644 AGGAGGAACATTGGCAGTGT 59.226 50.000 10.11 10.11 0.00 3.55
644 675 5.785940 GTGAGTAAATATAGGGGGATGGAGT 59.214 44.000 0.00 0.00 0.00 3.85
707 738 6.051717 GCTCTTGAATTAGCCATGAACTCTA 58.948 40.000 0.00 0.00 32.40 2.43
730 761 2.286872 CAATGCCTGACTCCATGACTC 58.713 52.381 0.00 0.00 0.00 3.36
746 777 1.875813 CTCGTGTGCAGATCGAGGC 60.876 63.158 20.38 0.00 44.54 4.70
842 873 2.045926 GGTTGAGCTGTCGCCCAT 60.046 61.111 0.00 0.00 36.60 4.00
896 927 4.899239 CGACGAGGGCATGGAGGC 62.899 72.222 0.00 0.00 43.27 4.70
1134 1167 0.770166 TGGATCAGGGTTGGACCACA 60.770 55.000 0.00 0.00 41.02 4.17
1143 1176 0.953471 GTTGGACCACATACGCAGCA 60.953 55.000 0.00 0.00 0.00 4.41
1193 1226 1.271102 GACGTTCAAGCTCCTCACTCT 59.729 52.381 0.00 0.00 0.00 3.24
1269 1302 2.048127 GGGAAGCACGACGAAGCT 60.048 61.111 12.46 12.46 44.31 3.74
1312 1350 3.499202 CCAGGGCCTCCGTAAGTACTATA 60.499 52.174 0.95 0.00 38.33 1.31
1829 1893 2.646719 GTGTAGTCACCGCCGTCA 59.353 61.111 0.00 0.00 38.51 4.35
1952 2049 4.126390 TCGTCGTCGTCGTCGCTC 62.126 66.667 15.28 2.62 44.86 5.03
1965 2062 4.180946 CGCTCTCGAGGACCACGG 62.181 72.222 13.56 2.78 38.10 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 1.586564 GAATGACCTCGACTCCGCG 60.587 63.158 0.00 0.00 35.37 6.46
104 105 1.008938 AGTCCTCCTACCTGGCAGAAT 59.991 52.381 17.94 6.25 35.26 2.40
105 106 0.413832 AGTCCTCCTACCTGGCAGAA 59.586 55.000 17.94 2.40 35.26 3.02
152 154 3.068691 GGGGGAAGAAAAGGCGGC 61.069 66.667 0.00 0.00 0.00 6.53
159 161 1.203570 AGCCTAAGGAGGGGGAAGAAA 60.204 52.381 0.00 0.00 43.97 2.52
167 169 2.844839 CGGGGAGCCTAAGGAGGG 60.845 72.222 0.00 0.00 43.97 4.30
387 390 0.957395 CGTGCTCATGAAGGCCACTT 60.957 55.000 5.01 0.00 40.34 3.16
416 419 0.110644 GCTCGAACTTTGCAGAACGG 60.111 55.000 0.00 0.00 0.00 4.44
555 577 2.700897 CAATGTTCCTCCTCCCTATCGT 59.299 50.000 0.00 0.00 0.00 3.73
560 582 0.846427 TGCCAATGTTCCTCCTCCCT 60.846 55.000 0.00 0.00 0.00 4.20
572 594 3.001414 CTCTCTTCTCACACTGCCAATG 58.999 50.000 0.00 0.00 0.00 2.82
573 595 2.027377 CCTCTCTTCTCACACTGCCAAT 60.027 50.000 0.00 0.00 0.00 3.16
577 599 0.248843 CCCCTCTCTTCTCACACTGC 59.751 60.000 0.00 0.00 0.00 4.40
583 605 1.081092 CCCACCCCCTCTCTTCTCA 59.919 63.158 0.00 0.00 0.00 3.27
644 675 2.158460 TGACTGTCACTCTTCTCCTCCA 60.158 50.000 6.36 0.00 0.00 3.86
707 738 1.064240 TCATGGAGTCAGGCATTGCAT 60.064 47.619 11.39 0.00 0.00 3.96
730 761 0.593518 CTAGCCTCGATCTGCACACG 60.594 60.000 4.80 0.00 0.00 4.49
746 777 1.224075 CGTGCCCATCTCATTGCTAG 58.776 55.000 0.00 0.00 0.00 3.42
842 873 4.728110 TCGGGTCTTCCTCGGCGA 62.728 66.667 10.14 10.14 0.00 5.54
947 980 1.477558 CCTTGCAGAAGTGAGTTGGGT 60.478 52.381 0.00 0.00 0.00 4.51
1129 1162 0.034756 TGAACTGCTGCGTATGTGGT 59.965 50.000 0.00 0.00 0.00 4.16
1134 1167 2.967599 TCTGATGAACTGCTGCGTAT 57.032 45.000 0.00 0.00 0.00 3.06
1143 1176 3.387374 AGCCGATCTTGATCTGATGAACT 59.613 43.478 8.70 0.09 0.00 3.01
1269 1302 1.079405 CTACTCCTTGGCGGCGAAA 60.079 57.895 12.98 2.67 0.00 3.46
1301 1334 8.851541 ACCATAGCAGACTCTATAGTACTTAC 57.148 38.462 0.00 0.00 35.56 2.34
1312 1350 3.133003 ACGCATAAACCATAGCAGACTCT 59.867 43.478 0.00 0.00 0.00 3.24
1448 1499 2.290071 TGTGGTAACCTCTTTGGCTAGC 60.290 50.000 6.04 6.04 40.22 3.42
1593 1650 4.722700 GCATCACGCCCCCAGTGT 62.723 66.667 0.00 0.00 40.84 3.55
1802 1866 1.133790 GGTGACTACACGCGGTTCTAT 59.866 52.381 12.47 0.00 46.77 1.98
1829 1893 1.012562 CGACGACGACGATGACGAT 60.013 57.895 15.32 0.00 41.06 3.73
1944 2041 2.818714 GGTCCTCGAGAGCGACGA 60.819 66.667 15.71 0.00 42.51 4.20
1945 2042 3.125573 TGGTCCTCGAGAGCGACG 61.126 66.667 15.71 0.00 46.44 5.12
1946 2043 2.486042 GTGGTCCTCGAGAGCGAC 59.514 66.667 15.71 12.71 46.44 5.19
1947 2044 3.125573 CGTGGTCCTCGAGAGCGA 61.126 66.667 15.71 0.00 46.44 4.93
1948 2045 4.180946 CCGTGGTCCTCGAGAGCG 62.181 72.222 15.71 10.13 46.44 5.03
1949 2046 4.500116 GCCGTGGTCCTCGAGAGC 62.500 72.222 15.71 10.33 43.62 4.09
1952 2049 4.477975 GACGCCGTGGTCCTCGAG 62.478 72.222 14.81 5.13 0.00 4.04


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.